3. Dimension reduction
Cankun Wang
09/21/2021
1 Set working dir
## [1] "Current working directory: C:/Users/flyku/Documents/GitHub/NOTCH1-scRNAseq/rmarkdown"2 Load data
3 Dimension reduction
Here we only want to visualize the sample differences in one UMAP. We adjusted UMAP neighbors and distance paramsters to make the visualization more ‘spread’
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 25000
## Number of edges: 900161
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## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9691
## Number of communities: 15
## Elapsed time: 3 seconds4 2D
5 3D
6 Session info
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
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## Matrix products: default
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## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936
## [2] LC_CTYPE=Chinese (Simplified)_China.936
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C
## [5] LC_TIME=Chinese (Simplified)_China.936
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotly_4.9.4.1 Polychrome_1.3.1 qs_0.25.1 here_1.0.1
## [5] patchwork_1.1.1 ggplot2_3.3.5 dplyr_1.0.6 cowplot_1.1.1
## [9] SeuratObject_4.0.2 Seurat_4.0.4
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_2.0-1 deldir_0.2-10
## [4] ellipsis_0.3.2 ggridges_0.5.3 rprojroot_2.0.2
## [7] spatstat.data_2.1-0 farver_2.1.0 leiden_0.3.9
## [10] listenv_0.8.0 ggrepel_0.9.1 RSpectra_0.16-0
## [13] fansi_0.5.0 codetools_0.2-18 splines_4.1.0
## [16] knitr_1.33 polyclip_1.10-0 jsonlite_1.7.2
## [19] ica_1.0-2 cluster_2.1.2 png_0.1-7
## [22] uwot_0.1.10 shiny_1.6.0 sctransform_0.3.2
## [25] spatstat.sparse_2.0-0 compiler_4.1.0 httr_1.4.2
## [28] assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
## [31] lazyeval_0.2.2 later_1.2.0 htmltools_0.5.1.1
## [34] tools_4.1.0 igraph_1.2.6 gtable_0.3.0
## [37] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
## [40] Rcpp_1.0.7 scattermore_0.7 jquerylib_0.1.4
## [43] vctrs_0.3.8 nlme_3.1-152 crosstalk_1.1.1
## [46] lmtest_0.9-38 xfun_0.25 stringr_1.4.0
## [49] globals_0.14.0 mime_0.10 miniUI_0.1.1.1
## [52] lifecycle_1.0.0 irlba_2.3.3 goftest_1.2-2
## [55] future_1.22.1 MASS_7.3-54 zoo_1.8-9
## [58] scales_1.1.1 spatstat.core_2.1-2 promises_1.2.0.1
## [61] spatstat.utils_2.2-0 parallel_4.1.0 RColorBrewer_1.1-2
## [64] yaml_2.2.1 reticulate_1.20 pbapply_1.4-3
## [67] gridExtra_2.3 sass_0.4.0 rpart_4.1-15
## [70] stringi_1.6.1 highr_0.9 rlang_0.4.11
## [73] pkgconfig_2.0.3 matrixStats_0.60.1 evaluate_0.14
## [76] lattice_0.20-44 ROCR_1.0-11 purrr_0.3.4
## [79] tensor_1.5 labeling_0.4.2 htmlwidgets_1.5.3
## [82] tidyselect_1.1.1 parallelly_1.27.0 RcppAnnoy_0.0.18
## [85] plyr_1.8.6 magrittr_2.0.1 R6_2.5.1
## [88] generics_0.1.0 DBI_1.1.1 pillar_1.6.2
## [91] withr_2.4.2 mgcv_1.8-36 fitdistrplus_1.1-5
## [94] scatterplot3d_0.3-41 survival_3.2-11 abind_1.4-5
## [97] tibble_3.1.2 future.apply_1.8.1 crayon_1.4.1
## [100] KernSmooth_2.23-20 utf8_1.2.1 RApiSerialize_0.1.0
## [103] spatstat.geom_2.2-0 rmarkdown_2.10 grid_4.1.0
## [106] data.table_1.14.0 digest_0.6.27 xtable_1.8-4
## [109] tidyr_1.1.3 httpuv_1.6.1 RcppParallel_5.1.4
## [112] stringfish_0.15.2 munsell_0.5.0 viridisLite_0.4.0
## [115] bslib_0.2.5.1